"growth condition: Inside Acanthamoeba"	"characteristics_ch1.1"
"growth condition: Outside Control"	"characteristics_ch2.1"
"Mixed model analysis was conducted as previously described (Madsen, et al., 2006) excluding slide region and slide-by-region interaction effects. The value column was not used for analysis or in publication. The normalized values for duplicate spots were averaged within each array to produce one normalized measure of expression for each of the probe sequences and each of the RNA samples. [mean log transformed median centered lowess normalized signal intensity]"	"data_processing.1"
"RNA was isolated from samples using the RNeasy Mini Kit (Qiagen). Prior to lysis all samples were incubated for 30 min on ice in RNA stop solution (0.1% SDS, 1% Acidic phenol, 19% ethanol, ice cold). The lysis and digestion protocol was followed with two 50 μl ddH20 elutions. Each sample was treated with 2 μl of DNase (Ambion, Austin, TX) at 37°C for 30 min. Samples were purified and concentrated using Microcon YM-30 columns (Millipore, Billerica, MA), and the quantity and purity were determined using an ND-1000 spectrophotometer (Nanodrop, Wilmington, DE). Samples were determined to be free of contaminating genomic DNA by absence of a band on a DNA electrophoresis gel after 30 rounds of PCR."	"extract_protocol_ch1.1"
"RNA was isolated from samples using the RNeasy Mini Kit (Qiagen). Prior to lysis all samples were incubated for 30 min on ice in RNA stop solution (0.1% SDS, 1% Acidic phenol, 19% ethanol, ice cold). The lysis and digestion protocol was followed with two 50 μl ddH20 elutions. Each sample was treated with 2 μl of DNase (Ambion, Austin, TX) at 37°C for 30 min. Samples were purified and concentrated using Microcon YM-30 columns (Millipore, Billerica, MA), and the quantity and purity were determined using an ND-1000 spectrophotometer (Nanodrop, Wilmington, DE). Samples were determined to be free of contaminating genomic DNA by absence of a band on a DNA electrophoresis gel after 30 rounds of PCR."	"extract_protocol_ch2.1"
"Escherichia coli"	"organism_ch1.1"
"Escherichia coli"	"organism_ch2.1"
"Escherichia coli O157:H7 EDL933 Inside Acanthamoeba"	"source_name_ch1.1"
"Escherichia coli O157:H7 EDL933 Outside Control"	"source_name_ch2.1"
"Escherichia coli O157:H7 EDL933 Inside Acanthamoeba vs. Control Slide 3"	"title.1"
"growth condition: Inside Acanthamoeba"	"characteristics_ch1.1"
"growth condition: Outside Control"	"characteristics_ch2.1"
"Escherichia coli"	"organism_ch1.1"
"Escherichia coli"	"organism_ch2.1"
"Escherichia coli O157:H7 EDL933 Inside Acanthamoeba"	"source_name_ch1.1"
"Escherichia coli O157:H7 EDL933 Outside Control"	"source_name_ch2.1"